Prepared system with lipid, water, protein, ligand, and ions

Dabble is a tool for building membrane protein systems. The ultimate goal of the project is to create an easy to use, one stop tool for system construction and parameterization.

Dabble includes both the main program dabble.py as well as a powerful API for building and parameterizing molecular dynamics systems.

To get started via Anaconda Python, use:

conda install -c rbetz dabble


  • Prepare membrane protein systems by inserting them into a membrane
  • Prepare solvated proteins by adding water
  • Add ions to neutralize and/or to desired concentration
  • Parameterize with CHARMM or AMBER parameter sets
  • Outputs files for simulation with AMBER or CHARMM
  • Automatic detection of post-translational modifications
  • Modified amino acids made easy
  • Ligands made easy! No more messing with atom names.

Supported Parameter Sets

  • [X] CHARMM
  • [X] AMBER
  • [ ] Gromacs

Supported Simulation Programs

  • [X] CHARMM
  • [X] AMBER
  • [X] Anton (via conversion)
  • [ ] Gromacs

Citing Dabble

There is no paper on Dabble yet. If you use Dabble, please cite it with the following DOI:


Dabble is a written by Robin Betz, in the Ron Dror lab at Stanford University. Bug finding is always apprecciated, as well as corner cases where your protein won't dabble.

Dabble is licensed under the GPLv2 license.

A lot of Dabble is powered by the VMD Python API.

API Documentation